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- PDB-7d1d: Crystal structure of Bacteroides thetaiotaomicron glutaminyl cycl... -

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Basic information

Entry
Database: PDB / ID: 7d1d
TitleCrystal structure of Bacteroides thetaiotaomicron glutaminyl cyclase bound to 1-benzylimidazole
ComponentsGlutamine cyclotransferase
KeywordsTRANSFERASE / Glutaminyl cyclase / METAL BINDING PROTEIN
Function / homologyGlutaminyl-peptide cyclotransferase-like / Peptidase M28 / Peptidase family M28 / acyltransferase activity / 1-BENZYL-1H-IMIDAZOLE / Glutamine cyclotransferase
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsHuang, K.-F. / Huang, J.-S. / Wu, M.-L. / Hsieh, W.-L. / Wang, A.H.-J.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-KPQ-109-ITAR-11, AS-SUMMIT-109, AS-KPQ-109-TPP2, AS-KPQ-109-TSPA Taiwan
CitationJournal: J.Mol.Biol. / Year: 2021
Title: A Unique Carboxylic-Acid Hydrogen-Bond Network (CAHBN) Confers Glutaminyl Cyclase Activity on M28 Family Enzymes.
Authors: Huang, K.F. / Huang, J.S. / Wu, M.L. / Hsieh, W.L. / Hsu, K.C. / Hsu, H.L. / Ko, T.P. / Wang, A.H.
History
DepositionSep 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamine cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7203
Polymers34,4961
Non-polymers2242
Water3,927218
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-32 kcal/mol
Surface area11980 Å2
Unit cell
Length a, b, c (Å)41.302, 78.536, 49.221
Angle α, β, γ (deg.)90.000, 114.510, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glutamine cyclotransferase


Mass: 34496.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BatF92_38840 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A679HSW5
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-1BN / 1-BENZYL-1H-IMIDAZOLE / 1-BENZYLIMIDAZOLE


Mass: 158.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.69 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M NaCl, 0.1 M Bis-Tris, pH 5.5, 25% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Sep 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→45 Å / Num. obs: 28784 / % possible obs: 99.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 15.9
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 2 / Num. unique obs: 2851 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FUU

4fuu


Resolution: 1.75→44.79 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.858 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1795 1447 5.1 %RANDOM
Rwork0.1329 ---
obs0.1352 26707 97.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.94 Å2 / Biso mean: 22.831 Å2 / Biso min: 11.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20.04 Å2
2---0.17 Å2-0 Å2
3---0.13 Å2
Refinement stepCycle: final / Resolution: 1.75→44.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2333 0 13 218 2564
Biso mean--38.31 34.75 -
Num. residues----294
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192406
X-RAY DIFFRACTIONr_bond_other_d0.0020.022238
X-RAY DIFFRACTIONr_angle_refined_deg1.3151.9433267
X-RAY DIFFRACTIONr_angle_other_deg0.9093.0015138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7085293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.47224.959121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.48615388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5091510
X-RAY DIFFRACTIONr_chiral_restr0.0810.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212778
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02565
X-RAY DIFFRACTIONr_rigid_bond_restr1.16234644
X-RAY DIFFRACTIONr_sphericity_free20.684581
X-RAY DIFFRACTIONr_sphericity_bonded5.23854721
LS refinement shellResolution: 1.751→1.796 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 88 -
Rwork0.193 1572 -
all-1660 -
obs--79.01 %

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